European and Japanese Chestnut RNASeq
Assembled EST sequences of Japanese chestnut, European chestnut, and combinations of the two have been provided by Susana Serrazina from BioFIG and Rita Costa from Instituto Nacional de Investigação Agrária e Veterinária.
Project Goal:
This project aims to gain knowledge of molecular mechanisms involved in tolerance to oomycete Phytophthora cinnamoni The root transcriptomes of Japanese chestnut (Castanea crenata, resistant to pathogen) and European chestnut (C. sativa, susceptible to pathogen) were sequenced during programmed conditions of infection. Non-inoculated controls in similar experimental conditions were also sequenced. Assembled EST sequences were compared at four levels: a) Inoculated C. crenata with non-inoculated control, b) C. sativa with non-inoculated control, c) Inoculated C. crenata with inoculated C. sativa, d) Non-inoculated C. crenata with non-noculated C. sativa. All collections and inoculations were conducted in Portugal.
Data:
ccn_csn
| Samples | Two samples (CCn/CSn) |
| Dates | Sequence in 2012-07-04 - Assembled in 2012-08 |
| Species | Castanea sativa,crenata |
| Description | Castanea sativa not infected vs Castanea crenata not infected (Non normalized samples). Assembled with 454 Newbler 2.6 |
| Version | 1 |
| # Reads | 412,054 |
| Total Bases | 147,694,000 |
| # Contigs (NT) | 13,873 |
| # Contigs (AA) | 13,873 |
Files:
- ccn_csn Contigs (NT Fasta File)
- ccn_csn Contigs (AA Fasta File)
- ccn_csn InterProScan Report (TSV format)
- ccn_csn GO Report (TSV format)
cci_csi
| Samples | Two samples (CCi/CSi) |
| Dates | Sequence in 2012-07-04 - Assembled in 2012-08 |
| Species | Castanea sativa,crenata |
| Description | Castanea sativa infected vs Castanea crenata infected (Non normalized samples). Assembled with 454 Newbler 2.6 |
| Version | 1 |
| # Reads | 441,233 |
| Total Bases | 155,780,000 |
| # Contigs (NT) | 12,985 |
| # Contigs (AA) | 12,574 |
Files:
- cci_csi Contigs (NT Fasta File)
- cci_csi Contigs (AA Fasta File)
- cci_csi InterProScan Report (TSV format)
- cci_csi GO Report (TSV format)
cci_ccn
| Samples | Two samples (CCi/CCn) |
| Dates | Sequence in 2012-07-04 - Assembled in 2012-08 |
| Species | Castanea crenata |
| Description | Castanea crenata infected vs Castanea crenata not infected (Non normalized samples). Assembled with 454 Newbler 2.6 |
| Version | 1 |
| # Reads | 445,434 |
| Total Bases | 155,688,992 |
| # Contigs (NT) | 13,451 |
| # Contigs (AA) | 13,451 |
Files:
- cci_ccn Contigs (NT Fasta File)
- cci_ccn Contigs (AA Fasta File)
- cci_ccn InterProScan Report (TSV format)
- cci_ccn GO Report (TSV format)
csi_csn
| Samples | Two samples (CSi/CSn) |
| Dates | Sequence in 2012-07-04 - Assembled in 2012-08 |
| Species | Castanea sativa |
| Description | Castanea sativa infected vs Castanea sativa not infected (Non normalized samples). Assembled with 454 Newbler 2.6 |
| Version | 1 |
| # Reads | 408,176 |
| Total Bases | 147,850,000 |
| # Contigs (NT) | 12,771 |
| # Contigs (AA) | 12,771 |
Files:
- csi_csn Contigs (NT Fasta File)
- csi_csn Contigs (AA Fasta File)
- csi_csn InterProScan Report (TSV format)
- csi_csn GO Report (TSV format)
ccn
| Samples | One sample (CCn) |
| Dates | Sequence in 2012-07-04 - Assembled in 2012-08 |
| Species | Castanea crenata |
| Description | Castanea crenatanot infected (Non normalized samples). Assembled with 454 Newbler 2.6 |
| Version | 1 |
| # Reads | 182,314 |
| Total Bases | 63,823,300 |
| # Contigs (NT) | 8,007 |
| # Contigs (AA) | 8,007 |
Files:
- ccn Contigs (NT Fasta File)
- ccn Contigs (AA Fasta File)
- ccn InterProScan Report (TSV format)
- ccn GO Report (TSV format)
cci
| Samples | One sample (CCi) |
| Dates | Sequence in 2012-07-04 - Assembled in 2012-08 |
| Species | Castanea crenata |
| Description | Castanea crenata infected (Non normalized samples). Assembled with 454 Newbler 2.6 |
| Version | 1 |
| # Reads | 220,412 |
| Total Bases | 77,175,000 |
| # Contigs (NT) | 8,061 |
| # Contigs (AA) | 8,061 |
Files:
- cci Contigs (NT Fasta File)
- cci Contigs (AA Fasta File)
- cci InterProScan Report (TSV format)
- cci GO Report (TSV format)
csi
| Samples | One sample (CSi) |
| Dates | Sequence in 2012-07-04 - Assembled in 2012-08 |
| Species | Castanea sativa |
| Description | Castanea sativa infected (Non normalized samples). Assembled with 454 Newbler 2.6 |
| Version | 1 |
| # Reads | 181,384 |
| Total Bases | 64,884,000 |
| # Contigs (NT) | 6,819 |
| # Contigs (AA) | 6,819 |
Files:
- csi Contigs (NT Fasta File)
- csi Contigs (AA Fasta File)
- csi InterProScan Report (TSV format)
- csi GO Report (TSV format)
csn
| Samples | One sample (CSn) |
| Dates | Sequence in 2012-07-04 - Assembled in 2012-08 |
| Species | Castanea sativa |
| Description | Castanea sativa not infected (Non normalized samples). Assembled with 454 Newbler 2.6 |
| Version | 1 |
| # Reads | 186,920 |
| Total Bases | 68,672,896 |
| # Contigs (NT) | 8,271 |
| # Contigs (AA) | 8,217 |
Files:
